Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery
and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
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VcfToAdpc takes a VCF, as generated by GtcToVcf and generates an Illumina 'adpc.bin' file from it. An adpc.bin file is a binary file containing genotyping array intensity data that can be exported by Illumina's GenomeStudio and Beadstudio analysis tools. The adpc.bin file is used as an input to VerifyIDintensity a tool for detecting and estimating sample contamination of Illumina genotyping array data.

Usage example:

Category
Genotyping Arrays Manipulation

Overview

A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).

VcfToAdpc (Picard) specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values: